An influence of the exchange rate on NOE intensities of a ligand: Application to 37kDa trp-holo-repressor/operator DNA complex

Abstract

: The cross peak intensities versus mixing times of 2D NOESY spectrum for a corepressor L-trp were simulated for the case of a ligand exchanging between free (AX) and bound ( ) forms in protein/DNA complex. The direct NOE (I(AX)) of the free ligand exhibited a small positive intensity indicative of the strong dominant influence of the bound ligand. The exchange-mediated NOE peak (I( )) was very sensitive to corepressor exchange. However, both diagonal (I( )) and direct NOE (I( )) intensities of the bound ligand were not affected much at initial stage. Both peaks were severely influenced by exchange at mixing times of greater than 100 ms. In conclusion, since the NOE intensity is a function of exchange rate, the exchange effect should be considered to properly extract accurate distance information for bound ligand in the presence of conformational exchange.